Sun 23 Dec 22:23:02 GMT 2018 ############### You are running ARP/wARP 8.0 ############### Working directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir Job ID is set to 1vkz-3.8-parrot-hancs X-ray data file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-3.8-parrot-hancs.mtz Sequence file /users/emra500/scratch/Dataset/hancsChltofom/1vkz-3.8-parrot-hancs.fasta Tracing mode WARPNTRACEPHASES Creating directory /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-hancs Accepted label: fp=FP Accepted label: sigfp=SIGFP Accepted label: phibest=hltofom.Phi_fom.phi Accepted label: fom=hltofom.Phi_fom.fom mtz labels taken: FP SIGFP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Parameter file /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-hancs/arp_warp_classic.par Job launched in /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-hancs ############### You are running ARP/wARP 8.0 ############### ============================================================ Please cite at least one of the publications below for the ARP/wARP application you are using: Lamzin VS, Wilson KS. (1993) Automated refinement of protein models. Acta Crystallogr D Biol Crystallogr. 49, 129-147 Morris RJ, Perrakis A. Lamzin VS. (2003) ARP/wARP and automatic interpretation of protein electron density maps. In Methods Enzymol. (Carter, C.W. & Sweet, R.M. eds.) 374, 229-244 Langer GG, Hazledine S, Wiegels T, Carolan C, Lamzin VS. (2013) Visual automated macromolecular model building. Acta Crystallogr D Biol Crystallogr. 69, 635-641 Use of Refmac is an essential part of model building with ARP/wARP. Please acknowledge the use of Refmac by citing the following publication: Murshudov GN, Skubak P, Lebedev AA, Pannu NS, Steiner RA, Nicholls RA, Winn MD, Long F, Vagin AA. (2011) REFMAC5 for the refinement of macromolecular crystal structures. Acta Crystallogr D Biol Crystallogr. 67, 355-367 ============================================================ Sun 23 Dec 22:23:12 GMT 2018 You are running ARP/wARP version 8.0 Entering warp_tracing.sh from COMMAND_LINE_SUBMISSION The working directory: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-hancs ARP/wARP software version: 8.0 The parameter file: /mnt/lustre/users/emra500/PipeliensFastaNoRFree/hancs/ArpWArp/wArpResults/WorkingDir/1vkz-3.8-parrot-hancs/arp_warp_classic.par ARP/wARP will run in subdirectory: temp_tracing Checking the estimated solvent content Computed solvent content is outside allowed range. Target number of residues/nucleotides is changed to 627 and 0 Target number of residues in the AU: 627 Target solvent content: 0.5993 Checking the provided sequence file Detected sequence length: 412 Maximum limit of NCS related copies: 60 Number of NCS-related molecules: 2 Adjusted target number of residues: 824 Adjusted target solvent content: 0.47 Input MTZ file: 1vkz-3.8-parrot-hancs.mtz.cad Column labels for model refinement: FP SIGFP Column labels to obtain initial map: FP hltofom.Phi_fom.phi hltofom.Phi_fom.fom Space group number: 4 Cell parameters: 63.745 78.443 85.018 90.000 95.062 90.000 Input sequence file: 1vkz-3.8-parrot-hancs.fasta_lf Building free atoms model in initial map for 6592 target number of atoms Had to go as low as 0.60 sigma, to complete atoms search. ARP/wARP will be iterated with REFMAC5 50 refinement / model update cycles will be run in total. Atoms will be removed below 1.0 sigma in 2mFoDFc map and added above 3.2 sigma in mFoDFc map. Refmac Refinement Parameters 3 REFMAC cycle(s) with 1.0 1.0 fractional shifts damping in each cycle. Conditional restraints will be used Weight for restraints is set to AUTO Solvent mask correction will be used Anisotropic scaling with no bulk solvent correction Model Building Parameters Main chain tracing will take place every 5 refinement / model update cycles. Side chain docking will be performed from autobuilding cycle number 1 NCS extension will be performed at every building cycle. NCS restraints will be applied at each refinement cycle. Loops will be built when appropriate and at the last cycle Resolution range: 19.959 3.800 Wilson plot Bfac: 52.34 Failed to save intermediate PDB 8080 reflections ( 96.28 % complete ) and 0 restraints for refining 7291 atoms. Observations/parameters ratio is 0.28 ------------------------------------------------------ Starting model: R = 0.2920 (Rfree = 0.000). ------------------------------------------------------ Cycle 0: After refmac, R = 0.2813 (Rfree = 0.000) for 7291 atoms. Found 40 (40 requested) and removed 70 (20 requested) atoms. ------------------------------------------------------ Building Cycle 1 Atomic shape factors 3.21 3.34 Search for helices and strands: 0 residues in 0 chains, 7380 seeds are put forward NCS extension: 0 residues added, 7380 seeds are put forward Round 1: 296 peptides, 61 chains. Longest chain 10 peptides. Score 0.283 Round 2: 381 peptides, 67 chains. Longest chain 17 peptides. Score 0.402 Round 3: 430 peptides, 68 chains. Longest chain 14 peptides. Score 0.482 Round 4: 435 peptides, 62 chains. Longest chain 16 peptides. Score 0.533 Round 5: 442 peptides, 58 chains. Longest chain 19 peptides. Score 0.571 Taking the results from Round 5 Chains 61, Residues 384, Estimated correctness of the model 0.0 % 7 chains (53 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13349 restraints for refining 5962 atoms. 11682 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 1: After refmac, R = 0.2349 (Rfree = 0.000) for 5962 atoms. Found 32 (32 requested) and removed 77 (16 requested) atoms. Cycle 2: After refmac, R = 0.2216 (Rfree = 0.000) for 5782 atoms. Found 32 (32 requested) and removed 43 (16 requested) atoms. Cycle 3: After refmac, R = 0.2272 (Rfree = 0.000) for 5710 atoms. Found 31 (31 requested) and removed 44 (15 requested) atoms. Cycle 4: After refmac, R = 0.1882 (Rfree = 0.000) for 5647 atoms. Found 20 (31 requested) and removed 24 (15 requested) atoms. Cycle 5: After refmac, R = 0.2053 (Rfree = 0.000) for 5594 atoms. Found 31 (31 requested) and removed 29 (15 requested) atoms. ------------------------------------------------------ Building Cycle 2 Atomic shape factors 3.22 3.35 Search for helices and strands: 0 residues in 0 chains, 5743 seeds are put forward NCS extension: 20 residues added (0 deleted due to clashes), 5763 seeds are put forward Round 1: 364 peptides, 68 chains. Longest chain 17 peptides. Score 0.362 Round 2: 426 peptides, 66 chains. Longest chain 18 peptides. Score 0.490 Round 3: 418 peptides, 64 chains. Longest chain 13 peptides. Score 0.491 Round 4: 457 peptides, 67 chains. Longest chain 23 peptides. Score 0.533 Round 5: 477 peptides, 72 chains. Longest chain 16 peptides. Score 0.530 Taking the results from Round 4 Chains 68, Residues 390, Estimated correctness of the model 0.0 % 7 chains (38 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 12449 restraints for refining 5669 atoms. 10834 conditional restraints added. Observations/parameters ratio is 0.36 ------------------------------------------------------ Cycle 6: After refmac, R = 0.2196 (Rfree = 0.000) for 5669 atoms. Found 31 (31 requested) and removed 68 (15 requested) atoms. Cycle 7: After refmac, R = 0.2071 (Rfree = 0.000) for 5555 atoms. Found 30 (30 requested) and removed 46 (15 requested) atoms. Cycle 8: After refmac, R = 0.2032 (Rfree = 0.000) for 5503 atoms. Found 30 (30 requested) and removed 38 (15 requested) atoms. Cycle 9: After refmac, R = 0.1899 (Rfree = 0.000) for 5464 atoms. Found 25 (30 requested) and removed 26 (15 requested) atoms. Cycle 10: After refmac, R = 0.1747 (Rfree = 0.000) for 5436 atoms. Found 22 (30 requested) and removed 25 (15 requested) atoms. ------------------------------------------------------ Building Cycle 3 Atomic shape factors 3.20 3.33 Search for helices and strands: 0 residues in 0 chains, 5610 seeds are put forward NCS extension: 18 residues added (3 deleted due to clashes), 5628 seeds are put forward Round 1: 356 peptides, 65 chains. Longest chain 12 peptides. Score 0.371 Round 2: 399 peptides, 61 chains. Longest chain 13 peptides. Score 0.481 Round 3: 450 peptides, 65 chains. Longest chain 16 peptides. Score 0.536 Round 4: 427 peptides, 61 chains. Longest chain 19 peptides. Score 0.527 Round 5: 426 peptides, 59 chains. Longest chain 19 peptides. Score 0.540 Taking the results from Round 5 Chains 62, Residues 367, Estimated correctness of the model 0.0 % 6 chains (42 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 12462 restraints for refining 5694 atoms. 10928 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 11: After refmac, R = 0.2217 (Rfree = 0.000) for 5694 atoms. Found 31 (31 requested) and removed 58 (15 requested) atoms. Cycle 12: After refmac, R = 0.1853 (Rfree = 0.000) for 5620 atoms. Found 23 (31 requested) and removed 28 (15 requested) atoms. Cycle 13: After refmac, R = 0.1693 (Rfree = 0.000) for 5574 atoms. Found 17 (30 requested) and removed 20 (15 requested) atoms. Cycle 14: After refmac, R = 0.1652 (Rfree = 0.000) for 5553 atoms. Found 10 (30 requested) and removed 20 (15 requested) atoms. Cycle 15: After refmac, R = 0.1522 (Rfree = 0.000) for 5529 atoms. Found 8 (30 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 4 Atomic shape factors 3.23 3.36 Search for helices and strands: 0 residues in 0 chains, 5675 seeds are put forward NCS extension: 16 residues added (0 deleted due to clashes), 5691 seeds are put forward Round 1: 398 peptides, 72 chains. Longest chain 11 peptides. Score 0.394 Round 2: 467 peptides, 73 chains. Longest chain 14 peptides. Score 0.507 Round 3: 483 peptides, 70 chains. Longest chain 14 peptides. Score 0.553 Round 4: 461 peptides, 69 chains. Longest chain 18 peptides. Score 0.525 Round 5: 483 peptides, 68 chains. Longest chain 16 peptides. Score 0.566 Taking the results from Round 5 Chains 69, Residues 415, Estimated correctness of the model 0.0 % 4 chains (28 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13027 restraints for refining 5850 atoms. 11342 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 16: After refmac, R = 0.2017 (Rfree = 0.000) for 5850 atoms. Found 32 (32 requested) and removed 61 (16 requested) atoms. Cycle 17: After refmac, R = 0.1811 (Rfree = 0.000) for 5768 atoms. Found 15 (32 requested) and removed 34 (16 requested) atoms. Cycle 18: After refmac, R = 0.1730 (Rfree = 0.000) for 5733 atoms. Found 12 (31 requested) and removed 25 (15 requested) atoms. Cycle 19: After refmac, R = 0.1653 (Rfree = 0.000) for 5704 atoms. Found 11 (31 requested) and removed 23 (15 requested) atoms. Cycle 20: After refmac, R = 0.1597 (Rfree = 0.000) for 5682 atoms. Found 8 (31 requested) and removed 17 (15 requested) atoms. ------------------------------------------------------ Building Cycle 5 Atomic shape factors 3.22 3.35 Search for helices and strands: 0 residues in 0 chains, 5831 seeds are put forward NCS extension: 13 residues added (0 deleted due to clashes), 5844 seeds are put forward Round 1: 380 peptides, 67 chains. Longest chain 13 peptides. Score 0.400 Round 2: 422 peptides, 60 chains. Longest chain 20 peptides. Score 0.526 Round 3: 448 peptides, 68 chains. Longest chain 15 peptides. Score 0.512 Round 4: 454 peptides, 58 chains. Longest chain 23 peptides. Score 0.588 Round 5: 428 peptides, 58 chains. Longest chain 23 peptides. Score 0.550 Taking the results from Round 4 Chains 60, Residues 396, Estimated correctness of the model 0.0 % 5 chains (61 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 12888 restraints for refining 5963 atoms. 11120 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 21: After refmac, R = 0.1999 (Rfree = 0.000) for 5963 atoms. Found 30 (32 requested) and removed 59 (16 requested) atoms. Failed to save intermediate PDB Cycle 22: After refmac, R = 0.1791 (Rfree = 0.000) for 5904 atoms. Found 23 (32 requested) and removed 75 (16 requested) atoms. Cycle 23: After refmac, R = 0.1722 (Rfree = 0.000) for 5836 atoms. Found 26 (32 requested) and removed 24 (16 requested) atoms. Cycle 24: After refmac, R = 0.1661 (Rfree = 0.000) for 5825 atoms. Found 12 (32 requested) and removed 24 (16 requested) atoms. Cycle 25: After refmac, R = 0.1600 (Rfree = 0.000) for 5803 atoms. Found 7 (31 requested) and removed 19 (15 requested) atoms. ------------------------------------------------------ Building Cycle 6 Atomic shape factors 3.22 3.35 Search for helices and strands: 0 residues in 0 chains, 5968 seeds are put forward NCS extension: 27 residues added (1 deleted due to clashes), 5995 seeds are put forward Round 1: 364 peptides, 68 chains. Longest chain 15 peptides. Score 0.362 Round 2: 407 peptides, 65 chains. Longest chain 15 peptides. Score 0.465 Round 3: 419 peptides, 58 chains. Longest chain 16 peptides. Score 0.536 Round 4: 427 peptides, 66 chains. Longest chain 16 peptides. Score 0.491 Round 5: 409 peptides, 58 chains. Longest chain 17 peptides. Score 0.520 Taking the results from Round 3 Chains 58, Residues 361, Estimated correctness of the model 0.0 % 7 chains (45 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13110 restraints for refining 5962 atoms. 11560 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 26: After refmac, R = 0.1950 (Rfree = 0.000) for 5962 atoms. Found 32 (32 requested) and removed 36 (16 requested) atoms. Cycle 27: After refmac, R = 0.1769 (Rfree = 0.000) for 5908 atoms. Found 14 (32 requested) and removed 27 (16 requested) atoms. Cycle 28: After refmac, R = 0.1706 (Rfree = 0.000) for 5874 atoms. Found 15 (32 requested) and removed 21 (16 requested) atoms. Cycle 29: After refmac, R = 0.1659 (Rfree = 0.000) for 5848 atoms. Found 8 (32 requested) and removed 20 (16 requested) atoms. Cycle 30: After refmac, R = 0.1648 (Rfree = 0.000) for 5827 atoms. Found 9 (32 requested) and removed 22 (16 requested) atoms. ------------------------------------------------------ Building Cycle 7 Atomic shape factors 3.23 3.36 Search for helices and strands: 0 residues in 0 chains, 5944 seeds are put forward NCS extension: 14 residues added (3 deleted due to clashes), 5958 seeds are put forward Round 1: 325 peptides, 59 chains. Longest chain 14 peptides. Score 0.360 Round 2: 379 peptides, 64 chains. Longest chain 16 peptides. Score 0.422 Round 3: 387 peptides, 63 chains. Longest chain 16 peptides. Score 0.445 Round 4: 417 peptides, 70 chains. Longest chain 13 peptides. Score 0.444 Round 5: 401 peptides, 59 chains. Longest chain 17 peptides. Score 0.499 Taking the results from Round 5 Chains 59, Residues 342, Estimated correctness of the model 0.0 % 5 chains (19 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13647 restraints for refining 5962 atoms. 12287 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 31: After refmac, R = 0.2069 (Rfree = 0.000) for 5962 atoms. Found 32 (32 requested) and removed 48 (16 requested) atoms. Cycle 32: After refmac, R = 0.2045 (Rfree = 0.000) for 5905 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 33: After refmac, R = 0.2087 (Rfree = 0.000) for 5873 atoms. Found 32 (32 requested) and removed 33 (16 requested) atoms. Cycle 34: After refmac, R = 0.1907 (Rfree = 0.000) for 5847 atoms. Found 32 (32 requested) and removed 30 (16 requested) atoms. Cycle 35: After refmac, R = 0.1829 (Rfree = 0.000) for 5832 atoms. Found 32 (32 requested) and removed 25 (16 requested) atoms. ------------------------------------------------------ Building Cycle 8 Atomic shape factors 3.16 3.29 Search for helices and strands: 0 residues in 0 chains, 5962 seeds are put forward NCS extension: 22 residues added (0 deleted due to clashes), 5984 seeds are put forward Round 1: 290 peptides, 57 chains. Longest chain 10 peptides. Score 0.306 Round 2: 357 peptides, 60 chains. Longest chain 19 peptides. Score 0.414 Round 3: 356 peptides, 57 chains. Longest chain 14 peptides. Score 0.436 Round 4: 362 peptides, 58 chains. Longest chain 14 peptides. Score 0.439 Round 5: 358 peptides, 55 chains. Longest chain 16 peptides. Score 0.455 Taking the results from Round 5 Chains 55, Residues 303, Estimated correctness of the model 0.0 % 4 chains (31 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13535 restraints for refining 5963 atoms. 12277 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 36: After refmac, R = 0.2094 (Rfree = 0.000) for 5963 atoms. Found 32 (32 requested) and removed 52 (16 requested) atoms. Cycle 37: After refmac, R = 0.1843 (Rfree = 0.000) for 5905 atoms. Found 20 (32 requested) and removed 41 (16 requested) atoms. Cycle 38: After refmac, R = 0.1709 (Rfree = 0.000) for 5876 atoms. Found 14 (32 requested) and removed 20 (16 requested) atoms. Cycle 39: After refmac, R = 0.1645 (Rfree = 0.000) for 5864 atoms. Found 15 (32 requested) and removed 24 (16 requested) atoms. Cycle 40: After refmac, R = 0.1621 (Rfree = 0.000) for 5847 atoms. Found 15 (32 requested) and removed 19 (16 requested) atoms. ------------------------------------------------------ Building Cycle 9 Atomic shape factors 3.21 3.34 Search for helices and strands: 0 residues in 0 chains, 5967 seeds are put forward NCS extension: 12 residues added (1 deleted due to clashes), 5979 seeds are put forward Round 1: 289 peptides, 58 chains. Longest chain 14 peptides. Score 0.295 Round 2: 317 peptides, 51 chains. Longest chain 14 peptides. Score 0.412 Round 3: 324 peptides, 53 chains. Longest chain 14 peptides. Score 0.409 Round 4: 310 peptides, 50 chains. Longest chain 17 peptides. Score 0.407 Round 5: 311 peptides, 50 chains. Longest chain 17 peptides. Score 0.409 Taking the results from Round 2 Chains 53, Residues 266, Estimated correctness of the model 0.0 % 7 chains (32 residues) have been docked in sequence ------------------------------------------------------ 8080 reflections ( 96.28 % complete ) and 13259 restraints for refining 5821 atoms. 12141 conditional restraints added. Observations/parameters ratio is 0.35 ------------------------------------------------------ Cycle 41: After refmac, R = 0.1840 (Rfree = 0.000) for 5821 atoms. Found 29 (32 requested) and removed 45 (16 requested) atoms. Cycle 42: After refmac, R = 0.1720 (Rfree = 0.000) for 5792 atoms. Found 20 (31 requested) and removed 22 (15 requested) atoms. Cycle 43: After refmac, R = 0.1704 (Rfree = 0.000) for 5784 atoms. Found 6 (31 requested) and removed 17 (15 requested) atoms. Cycle 44: After refmac, R = 0.1670 (Rfree = 0.000) for 5770 atoms. Found 13 (31 requested) and removed 19 (15 requested) atoms. Cycle 45: After refmac, R = 0.1625 (Rfree = 0.000) for 5760 atoms. Found 11 (31 requested) and removed 18 (15 requested) atoms. ------------------------------------------------------ Building Cycle 10 Atomic shape factors 3.26 3.39 Search for helices and strands: 0 residues in 0 chains, 5878 seeds are put forward NCS extension: 16 residues added (1 deleted due to clashes), 5894 seeds are put forward Round 1: 283 peptides, 60 chains. Longest chain 14 peptides. Score 0.264 Round 2: 335 peptides, 59 chains. Longest chain 17 peptides. Score 0.380 Round 3: 341 peptides, 59 chains. Longest chain 12 peptides. Score 0.392 Round 4: 338 peptides, 57 chains. Longest chain 12 peptides. Score 0.402 Round 5: 365 peptides, 60 chains. Longest chain 18 peptides. Score 0.428 Taking the results from Round 5 Last building cycle: Chain fragments will be rearranged Chains 61, Residues 305, Estimated correctness of the model 0.0 % 9 chains (45 residues) have been docked in sequence Sequence coverage is 14 % Consider running further cycles of model building using 1vkz-3_warpNtrace.pdb as input Building loops using Loopy2018 61 chains (305 residues) following loop building 9 chains (45 residues) in sequence following loop building ------------------------------------------------------ ---> Final restrained refinement block. No atom update. 8080 reflections ( 96.28 % complete ) and 13431 restraints for refining 5962 atoms. 12145 conditional restraints added. Observations/parameters ratio is 0.34 ------------------------------------------------------ Cycle 46: After refmac, R = 0.1971 (Rfree = 0.000) for 5962 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 47: After refmac, R = 0.1879 (Rfree = 0.000) for 5927 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 48: After refmac, R = 0.1853 (Rfree = 0.000) for 5902 atoms. Found 0 (32 requested) and removed 16 (16 requested) atoms. Cycle 49: After refmac, R = 0.1802 (Rfree = 0.000) for 5880 atoms. TimeTaking 75.07